src/hg/makeDb/trackDb/xenoEst.html 1.14

Index: src/hg/makeDb/trackDb/xenoEst.html
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/xenoEst.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/hg/makeDb/trackDb/xenoEst.html	20 Sep 2007 02:24:07 -0000	1.13
+++ src/hg/makeDb/trackDb/xenoEst.html	23 Jan 2010 00:53:45 -0000	1.14
@@ -1,86 +1,86 @@
 <H2>Description</H2>
 <P>
 This track displays translated blat alignments of expressed sequence tags 
 (ESTs) in <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/index.html" 
 TARGET=_blank>GenBank</A> from organisms other than $organism.
 ESTs are single-read sequences, typically about 500 bases in length, that 
 usually represent fragments of transcribed genes.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 This track follows the display conventions for 
 <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" 
 TARGET=_blank>PSL alignment tracks</A>. In dense display mode, the items that
 are more darkly shaded indicate matches of better quality. </P>
 <P>
 The strand information (+/-) for this track is in two parts.  The
 first + or - indicates the orientation of the query sequence whose
 translated protein produced the match.  The second + or - indicates the
 orientation of the matching translated genomic sequence.  Because the two
 orientations of a DNA sequence give different predicted protein sequences,
 there are four combinations.  ++ is not the same as --, nor is +- the same
 as -+.</P>
 <P>
 The description page for this track has a filter that can be used to change 
 the display mode, alter the color, and include/exclude a subset of items 
 within the track. This may be helpful when many items are shown in the track 
 display, especially when only some are relevant to the current task.  </P>
 <P>
 To use the filter:
 <OL>
 <LI>Type a term in one or more of the text boxes to filter the EST
 display. For example, to apply the filter to all ESTs expressed in a specific
 organ, type the name of the organ in the tissue box. To view the list of 
 valid terms for each text box, consult the table in the Table Browser that 
 corresponds to the factor on which you wish to filter. For example, the 
 &quot;tissue&quot; table contains all the types of tissues that can be 
 entered into the tissue text box. Multiple terms may be entered at once, 
 separated by a space. Wildcards may also be used in the
 filter.
 <LI>If filtering on more than one value, choose the desired combination
 logic. If &quot;and&quot; is selected, only ESTs that match all filter 
 criteria will be highlighted. If &quot;or&quot; is selected, ESTs that 
 match any one of the filter criteria will be highlighted.
 <LI>Choose the color or display characteristic that should be used to 
 highlight or include/exclude the filtered items. If &quot;exclude&quot; is 
 chosen, the browser will not display ESTs that match the filter criteria. 
 If &quot;include&quot; is selected, the browser will display only those 
 ESTs that match the filter criteria.
 </OL></P>
 <P>
 This track may also be configured to display base labeling, a feature that
 allows the user to display all bases in the aligning sequence or only those 
 that differ from the genomic sequence. For more information about this option,
 click 
 <A HREF="../goldenPath/help/hgBaseLabel.html" TARGET=_blank>here</A>.
 Several types of alignment gap may also be colored; 
 for more information, click 
 <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>.
 </P>
 
 <H2>Methods</H2>
 <P>
 To generate this track, the ESTs were aligned against the genome using 
 blat. When a single EST aligned in multiple places, the 
 alignment having the highest base identity was found.  Only alignments 
 having a base identity level within 0.5% of the best and at least 96% base 
 identity with the genomic sequence were kept.</P>
 
 <H2>Credits</H2>
 <P>
 This track was produced at UCSC from EST sequence data submitted to the 
 international public sequence databases by scientists worldwide.</P>
 
 <H2>References</H2>
 <P>
-Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and 
-Wheeler, D.L. 
-<A HREF="http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D23" 
-TARGET=_blank>GenBank: update</A>. <em>Nucleic Acids Res.</em> <B>32</B>,
-D23-6 (2004).</P>
+Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, 
+Wheeler DL. 
+<A HREF="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D23" 
+TARGET=_blank>GenBank: update</A>. <em>Nucleic Acids Res.</em> 
+2004 Jan 1;32(Database issue):D23-6.</P>
 <P>
-Kent, W.J.
+Kent WJ.
 <A HREF="http://www.genome.org/cgi/content/abstract/12/4/656" 
 TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.
-<em>Genome Res.</em> <B>12</B>(4), 656-664 (2002).</P>
+<em>Genome Res.</em> 2002 Apr;12(4):656-64.</P>